Physical exercise induces beneficial effects on cardiac autonomic nervous system (ANS) activity with higher vagal tone. Studies of gender-related differences in cardiac ANS function indicate higher vagal activity in young women than in men. The aim of this study was to assess in young élite athletes gender-linked ANS activity by using heart rate variability (HRV) analysis. The ECGs were recorded in 40 healthy young subjects, supine at rest, divided in 24 élite athletes (12 females, 12 males), matched according to the sports disciplines, and 16 controls (5 females, 11 males). For the HRV analysis Poincaré plot was evaluated from the tachograms. The SD1 parameter, used as a marker of vagal influence, SD2 parameter, correlated to sympathetic activity, and SD1/SD2 ratio, indicating the vago/sympathetic balance, were calculated. In the athletes, no significant sex-linked difference was observed in the mean heart rate (HR), in SD1 and SD2 parameters and in SD1/SD2 ratio. In the controls, there was no significant difference in the mean HR, whereas the SD1 parameter and the SD1/SD2 ratio were significantly higher in females compared to males. Comparing athletes to controls, the athletes presented lower mean HR and higher SD1/SD2 ratio. In conclusion, our results suggest no gender-related differences in cardiac ANS modulation of élite athletes with a shift in the vago-sympathetic balance towards relatively more vagal and less sympathetic activity, independently of the gender.